Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance.

Cong Cheng,Wangxiao Zhou,Jun Ying,Peiyao Zhang,Kexin Zhou,Xi Lin,Teng Xu,Danying Zhou,Peizhen Li,Qiyu Bao,Junwan Lu,Xu Dong,Changrui Qian,Kewei Li

doi:10.3389/fcimb.2021.663933

Abstract

Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.

Highlights

Delftia is a genus of opportunistic, Gram-negative, aerobic, motile, non-spore-forming and nonfermenting bacilli belonging to the family Comamonadaceae (Wen et al, 1999)
A clinical D. tsuruhatensis strain designated TR1180 was isolated from the Central Hospital of Lishui City, China
Phylogenetic trees based on the 16S Ribosomal RNAs (rRNAs) gene and whole-genome sequences showed that TR1180 belonged to the genus Delftia and exhibited the closest evolutionary relationship with D. tsuruhatensis NBRC 16741 (NZ_BCTO00000000) (Figure 1)

Summary

Introduction

Delftia is a genus of opportunistic, Gram-negative, aerobic, motile, non-spore-forming and nonfermenting bacilli belonging to the family Comamonadaceae (Wen et al, 1999). Members of the genus were initially classified into the genus Comamonas until 1999, when Wen et al, reevaluated their taxonomy and proposed a new genus named Delftia based on phylogenetic and phenotypic evidence (Wen et al, 1999) This genus is grouped into six species: D. acidovorans (Wen et al, 1999), D. tsuruhatensis (Shigematsu et al, 2003), D. lacustris (Jørgensen et al, 2009), D. litopenaei (Chen et al, 2012), D. deserti (Li et al, 2015) and D. rhizosphaerae (Carro et al, 2017), which reside in soil, water, sludge and human microflora (Lipuma et al, 2015). Some D. tsuruhatensis isolates have exhibited anti-biofilm activities (Singh et al, 2017) and resistance to heavy metals, such as zinc, lead and cadmium (Dorian et al, 2012; Lin et al, 2016)

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Conclusion